Contacts of the helix formed by residues 221 - 235 (chain B) in PDB entry 1EFA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A GLU* 4.8 15.7 - - - -
278A ASP* 5.7 0.2 - - - -
219B ASP* 2.8 23.6 + - - -
220B TRP* 1.3 79.3 - - - +
222B ALA* 1.3 62.4 + - - +
223B MET* 3.4 9.4 + - - +
224B SER* 2.6 36.7 + - - -
225B GLY 3.2 3.5 + - - -
248B GLN* 4.9 4.3 - - - +
249B MET* 3.4 5.4 - - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 5.2 2.6 - - - +
278A ASP* 4.0 23.7 + - - +
281A CYS* 3.7 23.3 - - + -
220B TRP 3.9 0.8 + - - -
221B SER* 1.3 73.1 - - - +
223B MET* 1.3 56.8 + - - +
225B GLY 3.1 0.9 + - - -
226B PHE* 2.8 24.9 + - - +
248B GLN* 3.1 30.4 + - - +
249B MET* 4.2 0.7 - - - +
251B LEU* 4.1 8.1 - - + -
252B GLY* 3.1 12.3 - - - +
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Residues in contact with MET 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 5.7 4.8 + - - +
280A SER* 4.4 13.2 - - - +
281A CYS* 3.8 18.7 - - - -
221B SER* 3.2 8.6 + - - +
222B ALA* 1.3 78.6 - - - +
224B SER* 1.3 58.9 + - - +
226B PHE* 3.1 34.4 + - + +
227B GLN* 2.8 60.5 + - + +
255B ARG* 4.6 7.4 - - - +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLY* 3.6 9.6 - - - -
219B ASP* 3.0 46.2 + - - -
221B SER* 2.6 25.2 + - - -
223B MET* 1.3 75.4 - - - +
225B GLY* 1.3 56.4 + - - +
227B GLN* 4.0 12.1 - - - +
228B GLN* 2.8 39.6 + - - +
249B MET* 3.6 3.6 - - - -
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 3.8 15.8 - - - +
221B SER 3.2 2.2 + - - -
222B ALA 3.1 7.4 + - - -
224B SER* 1.3 84.6 + - - +
226B PHE* 1.3 58.7 + - - +
229B THR* 3.0 30.8 + - - -
249B MET* 3.6 22.7 - - - -
252B GLY 3.7 6.7 - - - -
253B ALA 3.7 1.4 + - - -
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A CYS* 4.0 7.4 - - - -
222B ALA 2.8 13.0 + - - +
223B MET* 3.1 31.8 + - + +
225B GLY* 1.3 75.4 - - - +
227B GLN* 1.3 63.4 + - + +
230B MET* 3.0 54.9 + - + +
252B GLY* 3.2 16.3 - - - +
255B ARG* 3.3 52.9 - - + -
256B ALA* 3.5 35.9 - - + +
259B GLU* 3.7 9.0 - - - -
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B MET* 2.8 54.2 + - + +
224B SER* 3.9 11.4 - - - +
226B PHE* 1.3 75.5 - - + +
228B GLN* 1.3 69.6 - - - +
230B MET* 3.1 6.1 + - - +
231B GLN* 2.9 36.8 + - - +
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 3.8 24.0 - - + -
216B ARG* 3.2 37.6 + - + +
217B GLU 3.4 28.2 + - - +
218B GLY* 4.4 1.3 - - - -
224B SER* 2.8 26.0 + - - +
225B GLY 4.3 0.7 - - - +
227B GLN* 1.3 77.2 - - - +
229B THR* 1.3 63.9 + - - +
230B MET 3.2 0.2 + - - -
231B GLN* 3.3 25.0 + - - +
232B MET* 3.0 23.2 + - - +
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 3.7 3.8 - - - +
216B ARG* 6.0 0.4 - - - -
225B GLY 3.0 19.7 + - - -
228B GLN* 1.3 77.9 - - - +
230B MET* 1.3 59.9 + - - +
232B MET* 3.8 12.0 - - + +
233B LEU* 3.2 33.7 + - + +
242B MET* 3.2 39.0 - - + +
253B ALA* 3.4 15.4 - - - +
256B ALA* 3.8 21.1 - - + -
257B ILE* 4.3 4.3 - - + -
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Residues in contact with MET 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PHE* 3.0 46.2 + - + +
227B GLN* 3.1 7.6 + - - +
229B THR* 1.3 75.6 - - - +
231B GLN* 1.3 56.1 + - + +
233B LEU* 3.2 4.4 + - - +
234B ASN* 2.8 64.5 + - - +
256B ALA* 3.8 19.3 - - + +
259B GLU* 5.8 5.2 - - + +
260B SER* 4.0 20.9 - - - +
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.0 27.9 - - - +
227B GLN* 2.9 25.5 + - - +
228B GLN* 3.7 25.3 + - - +
230B MET* 1.3 76.2 - - + +
232B MET* 1.3 61.9 + - - +
234B ASN* 3.2 11.2 + - - +
235B GLU* 3.0 30.0 + - - +
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Residues in contact with MET 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ALA* 3.7 23.1 - - - -
214B ALA* 3.8 14.1 - - + -
216B ARG* 3.7 27.3 - - + +
228B GLN 3.0 17.3 + - - +
229B THR* 3.8 13.9 - - + +
231B GLN* 1.3 78.1 - - - +
233B LEU* 1.3 68.5 + - + +
235B GLU* 3.2 14.3 + - - +
237B ILE* 3.3 35.9 + - + +
239B PRO* 3.4 32.8 - - + -
242B MET* 3.9 27.6 - - + -
268B ILE* 5.6 0.9 - - + -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B THR* 3.2 32.5 + - + +
230B MET* 3.2 6.0 + - - +
232B MET* 1.3 82.6 - - + +
234B ASN* 1.3 64.0 + - - +
236B GLY* 3.0 18.4 + - - -
237B ILE 3.8 16.2 - - - +
238B VAL* 4.0 25.0 - - + +
256B ALA* 4.2 8.7 - - + +
257B ILE* 4.3 8.5 - - + -
260B SER* 3.5 31.9 - - - +
262B LEU* 4.7 4.7 - - + -
268B ILE* 4.3 12.8 - - + -
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Residues in contact with ASN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B MET* 2.8 54.3 + - - +
231B GLN* 3.2 9.2 + - - +
233B LEU* 1.3 70.0 - - - +
235B GLU* 1.3 59.0 + - + +
236B GLY 3.0 8.5 + - - -
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.3 36.6 + - - -
231B GLN* 3.0 14.9 + - - +
232B MET 3.5 6.9 - - - +
233B LEU 3.1 0.6 - - - -
234B ASN* 1.3 76.0 - - + +
236B GLY* 1.3 55.9 + - - +
237B ILE* 3.1 29.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il